Dual-beam instruments incorporate both an electron column and an ion column into a single instrument, and therefore allow the chemical vapor deposition (CVD) process to be either ion- or electron-beam assisted. Damage has been observed in the surface layers of specimens in which ion-beam assisted CVD processes have been employed. Cross-section transmission electron microscopy (TEM) has been used to compare (100) Si substrates on which Pt metal lines have been grown by ion- and electron-beam assisted CVD processes. The micrographs show that a 30 keV Ga+ ion beam, a 5 keV ion beam, and a 3 keV electron beam imparts 50 nm, 13 nm, and 3 nm of damage to the Si substrate, respectively. In addition, Au-Pd and Cr sputter coatings were evaluated for the prevention of ion-beam induced surface damage. TEM cross-section specimens revealed that Cr sputter coatings > 30 nm in thickness are sufficient to protect the (100) Si surface from the 30 keV Ga+ ion beam while Au-Pd sputter coatings up to 70 nm in thickness may be discontinuous and, therefore, will not protect surface regions from ion beam damage.